2I7D | pdb_00002i7d

Structure of Human cytosolic deoxyribonucleotidase in complex with deoxyuridine, AlF4 and Mg2+

• PDB DOI: https://doi.org/10.2210/pdb2I7D/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-08-30 Released: 2007-10-30 
• Deposition Author(s): Rinaldo-Matthis, A., Wallden, K., Nordlund, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.196 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Literature

Structures of Human and Murine cytosolic deoxyribonucleotidase: Insights into substrate specificity and catalysis

Wallden, K., Rinaldo-Matthis, A., Ruzzenente, B., Rampazzo, C., Bianchi, V., Nordlund, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.92 kDa 
• Atom Count: 3,909 
• Modeled Residue Count: 385 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'(3')-deoxyribonucleotidase, cytosolic type	A, B	193	Homo sapiens	Mutation(s): 0  EC: 3.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TCD5 (Homo sapiens) Explore Q8TCD5  Go to UniProtKB:  Q8TCD5
PHAROS:  Q8TCD5 GTEx:  ENSG00000125458

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DUR	E [auth A], H [auth B]	2'-DEOXYURIDINE C9 H12 N2 O5 MXHRCPNRJAMMIM-SHYZEUOFSA-N
ALF	D [auth A], G [auth B]	TETRAFLUOROALUMINATE ION Al F4 UYOMQIYKOOHAMK-UHFFFAOYSA-J
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.196 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.623	α = 68.92
b = 47.153	β = 81.69
c = 62.384	γ = 74.99

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
Deposition Author(s): Rinaldo-Matthis, A., Wallden, K., Nordlund, P.

Revision History  

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations